Starting phenix.real_space_refine (version: dev) on Thu Feb 23 16:08:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/02_2023/7mpg_23933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/02_2023/7mpg_23933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/02_2023/7mpg_23933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/02_2023/7mpg_23933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/02_2023/7mpg_23933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpg_23933/02_2023/7mpg_23933.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20366 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3497 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1636 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1635 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1636 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.30, per 1000 atoms: 0.55 Number of scatterers: 20366 At special positions: 0 Unit cell: (196.88, 202.23, 128.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4040 8.00 N 3390 7.00 C 12828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.04 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.05 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.05 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.04 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.05 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 500 " Time building additional restraints: 8.24 Conformation dependent library (CDL) restraints added in 3.0 seconds 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 48 sheets defined 21.1% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.516A pdb=" N LYS A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 201 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.790A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.800A pdb=" N VAL A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 369 through 372 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 491 through 512 Processing helix chain 'B' and resid 73 through 96 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.649A pdb=" N LYS B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.867A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.709A pdb=" N VAL B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 282' Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 369 through 372 Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 491 through 512 Processing helix chain 'C' and resid 73 through 96 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 removed outlier: 3.568A pdb=" N LYS C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 217 through 238 removed outlier: 3.884A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.709A pdb=" N VAL C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 282' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 369 through 372 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 491 through 512 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 187 through 189 No H-bonds generated for 'chain 'F' and resid 187 through 189' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.500A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 128 Processing helix chain 'G' and resid 183 through 189 removed outlier: 3.788A pdb=" N LYS G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.582A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.515A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 Processing helix chain 'I' and resid 183 through 189 removed outlier: 3.733A pdb=" N LYS I 188 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.692A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.536A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.900A pdb=" N LYS E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 312 removed outlier: 6.077A pdb=" N ILE A 309 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 48 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR A 311 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 10.231A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL A 300 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N MET A 289 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN A 302 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER A 287 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 287 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 244 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.563A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.625A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 308 through 312 removed outlier: 6.095A pdb=" N ILE B 309 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU B 48 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR B 311 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 10.259A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 56 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 190 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 300 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N MET B 289 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLN B 302 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER B 287 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 287 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 244 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.584A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.611A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AB5, first strand: chain 'C' and resid 308 through 312 removed outlier: 6.146A pdb=" N ILE C 309 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU C 48 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR C 311 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 10.151A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 190 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 300 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET C 289 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN C 302 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N SER C 287 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 287 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 244 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.657A pdb=" N ASN C 426 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.659A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP F 95 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.659A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG F 94 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG F 96 " --> pdb=" O MET F 100F" (cutoff:3.500A) removed outlier: 8.016A pdb=" N MET F 100F" --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.550A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.550A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AC7, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.581A pdb=" N GLU G 105 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 114 through 118 removed outlier: 6.174A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 144 through 149 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.305A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.387A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.231A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.526A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU I 33 " --> pdb=" O HIS I 49 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.526A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 115 through 118 removed outlier: 6.054A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 144 through 149 Processing sheet with id=AE3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.076A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.891A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.891A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AE8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.572A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU E 33 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N HIS E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.572A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 115 through 118 removed outlier: 5.921A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 144 through 149 950 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 8.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6565 1.35 - 1.48: 5041 1.48 - 1.61: 8994 1.61 - 1.73: 0 1.73 - 1.86: 144 Bond restraints: 20744 Sorted by residual: bond pdb=" CA MET D 82 " pdb=" CB MET D 82 " ideal model delta sigma weight residual 1.526 1.573 -0.047 1.26e-02 6.30e+03 1.39e+01 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ASP G 1 " pdb=" CA ASP G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASP I 1 " pdb=" CA ASP I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " ideal model delta sigma weight residual 1.808 1.861 -0.053 3.30e-02 9.18e+02 2.56e+00 ... (remaining 20739 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.97: 417 105.97 - 112.99: 11566 112.99 - 120.00: 6629 120.00 - 127.02: 9354 127.02 - 134.04: 191 Bond angle restraints: 28157 Sorted by residual: angle pdb=" CG1 VAL G 115 " pdb=" CB VAL G 115 " pdb=" CG2 VAL G 115 " ideal model delta sigma weight residual 110.80 121.97 -11.17 2.20e+00 2.07e-01 2.58e+01 angle pdb=" CA CYS B 313 " pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " ideal model delta sigma weight residual 114.40 123.45 -9.05 2.30e+00 1.89e-01 1.55e+01 angle pdb=" C LYS B 272 " pdb=" N LEU B 273 " pdb=" CA LEU B 273 " ideal model delta sigma weight residual 120.54 125.77 -5.23 1.35e+00 5.49e-01 1.50e+01 angle pdb=" CA CYS C 313 " pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " ideal model delta sigma weight residual 114.40 123.23 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA VAL G 115 " pdb=" CB VAL G 115 " pdb=" CG2 VAL G 115 " ideal model delta sigma weight residual 110.40 116.84 -6.44 1.70e+00 3.46e-01 1.43e+01 ... (remaining 28152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.58: 11864 22.58 - 45.16: 689 45.16 - 67.74: 54 67.74 - 90.32: 24 90.32 - 112.90: 1 Dihedral angle restraints: 12632 sinusoidal: 4940 harmonic: 7692 Sorted by residual: dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.46 -57.46 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS G 134 " pdb=" SG CYS G 134 " pdb=" SG CYS G 194 " pdb=" CB CYS G 194 " ideal model delta sinusoidal sigma weight residual 93.00 43.30 49.70 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" C2 NAG C 601 " pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " pdb=" C5 NAG C 601 " ideal model delta sinusoidal sigma weight residual -50.00 62.90 -112.90 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 12629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 3284 0.333 - 0.667: 0 0.667 - 1.000: 0 1.000 - 1.334: 0 1.334 - 1.667: 2 Chirality restraints: 3286 Sorted by residual: chirality pdb=" CG LEU I 94 " pdb=" CB LEU I 94 " pdb=" CD1 LEU I 94 " pdb=" CD2 LEU I 94 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.95e+01 chirality pdb=" CB VAL G 115 " pdb=" CA VAL G 115 " pdb=" CG1 VAL G 115 " pdb=" CG2 VAL G 115 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.45 2.00e-01 2.50e+01 5.28e+01 chirality pdb=" CA ILE C 292 " pdb=" N ILE C 292 " pdb=" C ILE C 292 " pdb=" CB ILE C 292 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3283 not shown) Planarity restraints: 3580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " 0.018 2.00e-02 2.50e+03 1.23e-02 3.76e+00 pdb=" CG TRP H 36 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 122 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO H 123 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 123 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 123 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 43 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO I 44 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 44 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 44 " -0.024 5.00e-02 4.00e+02 ... (remaining 3577 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 192 2.51 - 3.10: 16050 3.10 - 3.70: 30894 3.70 - 4.30: 43610 4.30 - 4.90: 72914 Nonbonded interactions: 163660 Sorted by model distance: nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 1.908 2.440 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 1.917 2.440 nonbonded pdb=" OG1 THR C 267 " pdb=" OD1 ASP C 269 " model vdw 1.935 2.440 nonbonded pdb=" OG1 THR B 267 " pdb=" OD1 ASP B 269 " model vdw 1.943 2.440 nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 1.964 2.440 ... (remaining 163655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 213)) selection = (chain 'F' and (resid 2 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 213)) selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 12828 2.51 5 N 3390 2.21 5 O 4040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.510 Check model and map are aligned: 0.330 Process input model: 54.170 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 20744 Z= 0.215 Angle : 0.710 11.174 28157 Z= 0.413 Chirality : 0.058 1.667 3286 Planarity : 0.004 0.051 3579 Dihedral : 13.488 112.901 7574 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.17), residues: 2610 helix: 0.18 (0.26), residues: 417 sheet: -0.62 (0.18), residues: 907 loop : -1.27 (0.17), residues: 1286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 0.3276 time to fit residues: 340.4224 Evaluate side-chains 405 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 109 optimal weight: 0.1980 chunk 67 optimal weight: 0.3980 chunk 133 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 0.3980 chunk 237 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 81 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 277 ASN B 302 GLN B 460 ASN C 277 ASN C 302 GLN F 76 ASN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 76 ASN I 3 GLN I 124 GLN D 76 ASN D 200 HIS E 124 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 20744 Z= 0.267 Angle : 0.699 10.285 28157 Z= 0.362 Chirality : 0.047 0.346 3286 Planarity : 0.005 0.055 3579 Dihedral : 5.842 108.528 2829 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.75 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2610 helix: 0.72 (0.25), residues: 429 sheet: -0.55 (0.17), residues: 912 loop : -1.08 (0.17), residues: 1269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 423 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 41 residues processed: 466 average time/residue: 0.3030 time to fit residues: 220.1276 Evaluate side-chains 372 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 331 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1766 time to fit residues: 17.1590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 197 optimal weight: 0.0970 chunk 161 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 237 optimal weight: 30.0000 chunk 256 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 190 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 302 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 20744 Z= 0.258 Angle : 0.664 12.663 28157 Z= 0.343 Chirality : 0.046 0.231 3286 Planarity : 0.005 0.050 3579 Dihedral : 5.745 108.239 2829 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.83 % Favored : 95.02 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2610 helix: 1.03 (0.26), residues: 429 sheet: -0.47 (0.17), residues: 910 loop : -0.97 (0.18), residues: 1271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 413 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 29 residues processed: 450 average time/residue: 0.3169 time to fit residues: 221.9317 Evaluate side-chains 367 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 338 time to evaluate : 2.589 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1889 time to fit residues: 13.8919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 225 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN F 76 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 20744 Z= 0.255 Angle : 0.644 12.086 28157 Z= 0.334 Chirality : 0.045 0.253 3286 Planarity : 0.005 0.049 3579 Dihedral : 5.669 108.018 2829 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2610 helix: 1.20 (0.26), residues: 429 sheet: -0.36 (0.17), residues: 920 loop : -0.99 (0.18), residues: 1261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 382 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 41 residues processed: 419 average time/residue: 0.3150 time to fit residues: 206.1067 Evaluate side-chains 375 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 334 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1899 time to fit residues: 17.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 174 optimal weight: 0.0030 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN D 76 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 20744 Z= 0.275 Angle : 0.652 10.027 28157 Z= 0.338 Chirality : 0.045 0.270 3286 Planarity : 0.005 0.048 3579 Dihedral : 5.730 108.170 2829 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.02 % Favored : 94.83 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.17), residues: 2610 helix: 1.07 (0.26), residues: 435 sheet: -0.39 (0.17), residues: 906 loop : -0.98 (0.18), residues: 1269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 378 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 406 average time/residue: 0.3212 time to fit residues: 202.9909 Evaluate side-chains 363 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 337 time to evaluate : 2.337 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1920 time to fit residues: 12.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 20744 Z= 0.217 Angle : 0.637 11.426 28157 Z= 0.330 Chirality : 0.045 0.310 3286 Planarity : 0.005 0.050 3579 Dihedral : 5.649 108.327 2829 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2610 helix: 1.37 (0.26), residues: 417 sheet: -0.40 (0.17), residues: 915 loop : -0.95 (0.18), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 365 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 381 average time/residue: 0.3432 time to fit residues: 202.6239 Evaluate side-chains 347 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 326 time to evaluate : 2.460 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1936 time to fit residues: 11.0716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 212 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 251 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 105 GLN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 20744 Z= 0.314 Angle : 0.681 10.566 28157 Z= 0.352 Chirality : 0.046 0.304 3286 Planarity : 0.005 0.048 3579 Dihedral : 5.807 108.010 2829 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2610 helix: 1.24 (0.26), residues: 417 sheet: -0.52 (0.17), residues: 918 loop : -1.03 (0.18), residues: 1275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 356 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 376 average time/residue: 0.3261 time to fit residues: 188.7526 Evaluate side-chains 354 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 328 time to evaluate : 2.410 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1787 time to fit residues: 12.0635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 20744 Z= 0.227 Angle : 0.666 13.832 28157 Z= 0.339 Chirality : 0.045 0.303 3286 Planarity : 0.005 0.047 3579 Dihedral : 5.708 108.368 2829 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.94 % Favored : 94.90 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2610 helix: 1.36 (0.26), residues: 417 sheet: -0.56 (0.17), residues: 924 loop : -1.03 (0.18), residues: 1269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 366 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 378 average time/residue: 0.3372 time to fit residues: 195.8571 Evaluate side-chains 360 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 344 time to evaluate : 2.461 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1858 time to fit residues: 9.0121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 10.0000 chunk 241 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 221 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 20744 Z= 0.258 Angle : 0.686 13.330 28157 Z= 0.350 Chirality : 0.045 0.308 3286 Planarity : 0.005 0.054 3579 Dihedral : 5.754 108.305 2829 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.29 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2610 helix: 1.27 (0.26), residues: 414 sheet: -0.60 (0.17), residues: 927 loop : -1.04 (0.18), residues: 1269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 354 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 357 average time/residue: 0.3434 time to fit residues: 189.0892 Evaluate side-chains 344 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 334 time to evaluate : 2.470 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1941 time to fit residues: 6.9896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 172 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 20744 Z= 0.339 Angle : 0.729 13.829 28157 Z= 0.373 Chirality : 0.047 0.319 3286 Planarity : 0.005 0.088 3579 Dihedral : 5.947 108.105 2829 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.17 % Favored : 93.68 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2610 helix: 0.89 (0.26), residues: 432 sheet: -0.64 (0.17), residues: 932 loop : -1.12 (0.18), residues: 1246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 339 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 345 average time/residue: 0.3417 time to fit residues: 183.5508 Evaluate side-chains 327 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 318 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2075 time to fit residues: 6.8924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 26 optimal weight: 0.0970 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.155079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109523 restraints weight = 37204.757| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.12 r_work: 0.3330 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 20744 Z= 0.247 Angle : 0.696 13.011 28157 Z= 0.354 Chirality : 0.046 0.325 3286 Planarity : 0.005 0.077 3579 Dihedral : 5.864 108.409 2829 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.44 % Favored : 94.41 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2610 helix: 0.93 (0.26), residues: 432 sheet: -0.57 (0.17), residues: 932 loop : -1.10 (0.18), residues: 1246 =============================================================================== Job complete usr+sys time: 4995.89 seconds wall clock time: 91 minutes 29.96 seconds (5489.96 seconds total)